A database of 18S rRNA metabarcodes
Version: 2.1.0 - 59 datasets
Release date: 2023-05-16
Presentation
MetaPR2 is a database of published 18S rRNA metabarcodes that have been reprocessed and assigned using PR2.
Acessing the database
Access to the database to map, search and download the barcodes can be done in three different ways:
Using a web interface.
Download the R package and launch the shiny application.
1 - Web interface
- Launch in your browser: http://shiny.metapr2.org
- Help : https://pr2database.github.io/metapr2-shiny/articles/
2 - metaPR2 shiny R package
Install the package from GitHub
install.packages(devtools)
devtools::install_github("pr2database/metapr2-shiny")Note: You may have to install some packages required by metapr2 if they are not installed on your machine
Alternatively install from R-universe
No need in this case to install package devtools
# Enable repository from pr2database
options(repos = c(
pr2database = 'https://pr2database.r-universe.dev',
CRAN = 'https://cloud.r-project.org'))
# Download and install metapr2 in R
install.packages('metapr2')Launch shiny interface with function run_app()
metapr2::run_app()Help
Extensive help is provided here.
Errors
Please report errors in the Issues page of the metaPR2 database.
Citation
Vaulot, D., Sim, C.W.H., Ong, D., Teo, B., Biwer, C., Jamy, M., Lopes dos Santos, A., 2022. metaPR2: a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists. Molecular Ecology Resources 22, 3188–3201. https://doi.org/10.1111/1755-0998.13674
Resources
Website: https://shiny.metapr2.org/
Source code: https://github.com/pr2database/metapr2-shiny
Docker (only version <= 1.0.2): https://hub.docker.com/repository/docker/vaulot/metapr2
Maintainer
- Daniel Vaulot: vaulot@gmail.com